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Sample GSM309820 Query DataSets for GSM309820
Status Public on Aug 05, 2008
Title L 9D HCHR
Sample type RNA
 
Source name Liver tissue, 9D high caloric diet (with addition of hydrogenated coconut oil) plus 0.04% resveratrol, ad libitum
Organism Mus musculus
Characteristics Strain: C57BL/6NIA, Gender: Male, Tissue: Liver, Age: 11months
Treatment protocol Starting at one year of age, fed a high caloric AIN-93G diet (with addition of hydrogenated coconut oil) plus 0.04% resveratrol, ad libitum.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen RNAeasy Mini kit
Label biotin
Label protocol standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description Liver 9D HCHR
Data processing Data was extracted using the Illumina BeadStudio software(v1). Any spots at or below the background were filtered out using an Illumina detection score of 0.98 and below. The natural log of all remaining genes were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores provided as supplementary file.
 
Submission date Aug 04, 2008
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6103
Series (1)
GSE11845 Resveratrol Diet Aging (Heart, Liver, Muscle and Fat Tissue)

Data table header descriptions
ID_REF
RAW_VALUE raw intensity value from Beadstudio software
VALUE Z transformation of the natural log of the raw intensity values

Data table
ID_REF RAW_VALUE VALUE
ILMN_1212602
ILMN_1212605 152.2 -0.1104283
ILMN_1212607 95.6 -0.6895425
ILMN_1212612 95.9 -0.6856407
ILMN_1212616
ILMN_1212619 92.8 -0.7265619
ILMN_1212626 99.4 -0.6409998
ILMN_1212628
ILMN_1212632 117.7 -0.4305526
ILMN_1212636 397.3 1.0844767
ILMN_1212637 1246.5 2.50840965
ILMN_1212644
ILMN_1212645 2046.8 3.12602416
ILMN_1212646 353.6 0.93936231
ILMN_1212648 113.9 -0.4714226
ILMN_1212672 158.3 -0.0614906
ILMN_1212681
ILMN_1212682 101.2 -0.61865
ILMN_1212683
ILMN_1212685

Total number of rows: 24600

Table truncated, full table size 605 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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